PyMol Tutorial

Download the latest PyMol versionFree educational license: http://pymol.org/edu/?q=educational/

Start PyMolI should more or less look like this:

The interface

Mouse actions

Command line

NamesPanel

Viewer

Mouse settingsSelect the type of mouse you are using, on a laptop go for “1 button viewing”

Loading a protein model - Option 1

• Download the model from a protein database• http://www.rcsb.org/pdb/home/home.do

• Load into PyMol, via command line:• “cd desktop” in case your file is on your desktop• “load 1b01.pdb”

Search

DownloadPDB format

Loading a protein model - Option 2

• Load straight into PyMol via command line• “fetch 1b01”

Actions

A: ActionS: ShowH: HideL: LabelC: Color

Pretty cartoon view

Subset selectionDisplay the sequence of your object: Display -> Sequence On

Select all DNA residuesClick and drag in the Sequence Bar

Save this object sub setClick on A -> Rename Selection. Type DNA and press enter

Now you can modify this partFor example, hide the DNA strand: H -> everything

The DNA part is now gone

Or Show DNA as SticksClick on S -> as: -> sticks

Or Show as SpheresClick on S -> as: -> spheres

Save an imageFile -> Save Image As -> PNG

These slides are published by Waag Society under CC-BY-SA 4.0 license